From c4f78dbfb07e296af41392b54deabde084e99f0a Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 3 May 2022 15:55:59 -0700 Subject: [PATCH] update to Cancogen vocabulary And marking PHAC Dexa, GRDI and GISAID templates as published. --- script/main.js | 8 ++++---- template/canada_covid19/data.js | 1 + template/canada_covid19/data.tsv | 6 ++++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/script/main.js b/script/main.js index 635b016f..e2bd773e 100644 --- a/script/main.js +++ b/script/main.js @@ -11,13 +11,13 @@ * main.html?template=test_template * */ -const VERSION = '0.15.4'; +const VERSION = '0.15.5'; const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION; const TEMPLATES = { 'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'}, - 'PHAC Dexa (ALPHA)': {'folder': 'phac_dexa', 'status': 'draft'}, - 'GRDI (ALPHA)': {'folder': 'grdi', 'status': 'draft'}, - 'GISAID (ALPHA)': {'folder': 'gisaid', 'status': 'draft'}, + 'PHAC Dexa': {'folder': 'phac_dexa', 'status': 'published'}, + 'GRDI': {'folder': 'grdi', 'status': 'published'}, + 'GISAID': {'folder': 'gisaid', 'status': 'published'}, 'PHA4GE': {'folder': 'pha4ge', 'status': 'published'} }; // Currently selected cell range[row,col,row2,col2] diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index b72d3b38..786ddeb3 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -418,6 +418,7 @@ var DATA = [ "Public Health Ontario (PHO)": {}, "Queen's University / Kingston Health Sciences Centre": {}, "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": {}, + "Shared Hospital Laboratory": {}, "St. John's Rehab at Sunnybrook Hospital": {}, "Switch Health": {}, "Sunnybrook Health Sciences Centre": {}, diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index d8d4ae17..a05faa87 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -1,5 +1,4 @@ Ontology ID Meaning (LinkML) parent class label datatype source data status requirement min value max value capitalize pattern description guidance examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -ID SC % GENEPIO:0001122 Database Identifiers GENEPIO:0001123 Database Identifiers specimen collector sample ID xs:unique Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID GENEPIO:0001202 Database Identifiers third party lab service provider name xs:token The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 @@ -1075,6 +1074,7 @@ GENEPIO:0100183 gene name 1 SARS-COV-2 5' UTR sample collected by Public Health Ontario (PHO) sample collected by Queen's University / Kingston Health Sciences Centre sample collected by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + sample collected by Shared Hospital Laboratory sample collected by St. John's Rehab at Sunnybrook Hospital sample collected by Switch Health sample collected by Sunnybrook Health Sciences Centre @@ -1352,4 +1352,6 @@ GAZ:00009572 geo_loc_name (country) West Bank GAZ:00000564 geo_loc_name (country) Western Sahara GAZ:00005284 geo_loc_name (country) Yemen GAZ:00001107 geo_loc_name (country) Zambia -GAZ:00001106 geo_loc_name (country) Zimbabwe \ No newline at end of file +GAZ:00001106 geo_loc_name (country) Zimbabwe + + \ No newline at end of file